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| == The Basic Idea ==
| | #REDIRECT [[TMT_Thesis_Project]] |
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| We have the naive idea that somehow you should be able to get more information out of a signaling pathway in the course of a given experiment by exposing the pathway to a time-varying stimulus, rather than the standard step-increase in stimulus. The idea would be to use time-dependent stimulation in conjunction with a model of the pathway to more rapidly evaluate and test hypotheses. We are using the yeast (''Saccharomyces cerevisiae'') pheromone signal transduction pathway as a model system on which to develop these ideas/technologies. It is an ideal system because it is a well-studied prototype for signal transduction in higher eukaryotes.
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| == Our Approach ==
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| We're using custom microfluidic devices, based on technologies developed by the [http://thebigone.stanford.edu/ Quake lab] at Stanford, to deliver time varying concentrations of the peptide pheromone, alpha factor, to immobilized cells. The microfluidic chip can be mounted on a microscope stage, and the cells response to the stimulus observed via fluorecent reporters in the pathway.
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| == Parameter Estimation ==
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| One obvious use for this technology would be to use the experimental results and a model of the pathway to attempt to constrain model parameters. This essentially comes down to estimating concentrations of proteins and rate constants from the experimental data. Since we're not so interested in the process of parameter estimation from data as we are interested in what the parameters are (and how to design experiments that will give us good numbers), we'll probably just use some off-the-shelf tools to do this for us.
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| == Experimental Design ==
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| This is an area that we're very interested. How can we select (time-varying) inputs to maximize the 'usefulness' of the data that we will obtain? We've got some ideas, but since this is a core thrust of [[User:Tmt|my]] thesis, and until they're better fleshed out (i.e. I've got a good head start), they shall not be mentioned here...
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| == Main Persons Working on This ==
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| Well, most of this page has been written in the plural with the hopes that at some point, we will have collaborators working with us on the time-dependent analysis (though it should be said that we have many collaborators working with us on biology, modeling, and other fronts who have been infinitely helpful). But for now, we = [[User:Tmt|Ty Thomson]].
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